Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery
and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
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Existence of a de novo mutation in at least one of the given families (hiConfDeNovo, loConfDeNovo)

Category
Variant Annotations

Overview

Existence of a de novo mutation in at least one of the given families

This annotation uses the genotype information from individuals in family trios to identify possible de novo mutations and the sample(s) in which they occur. This works best if the genotypes have been processed according to the Genotype Refinement workflow.

Caveats

The calculation assumes that the organism is diploid.

This annotation requires a valid pedigree file.

Only reports possible de novos for children whose genotypes have not been tagged as filtered (which is most appropriate if parent likelihoods
have already been factored in using PhaseByTransmission).

When multiple trios are present, the annotation is simply the maximum of the likelihood ratios, rather than the strict 1-Prod(1-p_i) calculation, as this can scale poorly for uncertain sites and many trios.

This annotation can only be used from the Variant Annotator. If you attempt to use it from the UnifiedGenotyper, the run will fail with an error message to that effect. If you attempt to use it from the HaplotypeCaller, the run will complete successfully but the annotation will not be added to any variants.

Related annotations

MVLikelihoodRatio evaluates whether a site is transmitted from parents to offspring according to Mendelian rules or not.